| -rescale -0.1,5.2 | Rescale data to average and standard deviation after filtering. |
| -median 3 | Median filter: kernel edge size. |
| -peak 5 | Peak filter: kernel edge size. |
| -gradient | Gradient filter (3x3x3). |
| -laplacian | Laplacian filter (3x3x3). |
| -denoise 2,0.4 | Denoising filter: distance and density difference sigmas. |
| -rollingball 5,4.3 | Rolling ball filter: radius and density scaling (default scaling=1). |
| -variance 5,var.img | Weigh image with local variance in a kernel of a given size, output variance image. |
| -extremes his | Filter image extremes: his=histogram-based, mg=for micrograph. |
| -replacemaxima 1.5 | Replace maxima above the given threshold with surrounding average. |
| -bandpass 25.3,200,0.02 | Bandpass filter: resolution limits (angstrom) and band edge width (1/angstrom). |
| -amplitude 8.3 | Amplitude filter: setting all amplitudes below the threshold to zero. |
| -phasesonly | Set all amplitudes to one. |
| -Bfactor 44,25.3,20 | B-factor application: B-factor (A^2), high resolution limit (A,optional) |
| and constant factor resolution limit (A). |
| Multiplied in reciprocal space by exp(-B-factor/4 * s^2) up to the first |
| resolution limit, and then kept constant up to the second limit. |
| -gaussratio 60,35,0.2 | Reciprocal space ratio of gaussians amplitude adjustment (B1,B2,a). |
| Ratio = exp(-B2/4*s^2) / ((1-a) + a*exp(-B1/4*s^2)). |
| |